Compositions and methods using cas9 with enhanced spacer acquisition function

ABSTRACT

Provided are Cas9 enzymes that have mutations that enhance their properties, relative to un-mutated Cas9. The altered Cas9 enzymes exhibit i) an increased rate of spacer acquisition, or ii) increased cleavage efficiency of targets with NAG PAMs, or a combination of i) and ii). The altered Cas9 enzymes comprise an amino acid substitution of 1473 and K500 in a  Streptococcus pyogenes  or similar Cas9 enzyme. Also provided are polynucleotides, including expression vectors that encode the Cas9 enzymes, cells that contain the polynucleotides, and methods of making and using such cells. The disclosure includes tagging, or labelling bacteria, and for enhancing phage acquired immunity in bacteria, such as those used in industrial processes, including the food and beverage industry, such as the dairy industry. The food products are also included.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. provisional application No. 62/435,406, filed Dec. 16, 2016, the disclosure of which is incorporated herein by reference.

FIELD

The present disclosure relates generally to Clustered regularly interspaced short palindromic repeat (CRISPR) systems, and more particularly to compositions and methods involving an improved Cas9 nuclease with enhanced spacer acquisition properties.

BACKGROUND

Clustered regularly interspaced short palindromic repeat (CRISPR) loci and their associated (Cas) proteins protect bacteria and archaea against their viruses (Barrangou et al., 2007) and plasmids (Marraffini and Sontheimer, 2008). In the first step of the CRISPR immune response, a very low proportion of the infected cells acquire a short sequence, known as a spacer sequence, of the invading genome in between the repeats of the CRISPR array (Barrangou et al., 2007). Spacer acquisition is catalyzed by the Cas1/Cas2 integration complex (Nunez et al., 2014; Nunez et al., 2015; Yosef et al., 2012) and results in the immunization of the host (Barrangou et al., 2007). In the second step of the CRISPR immune response, spacer sequences are transcribed and processed into a small RNA known as the CRISPR RNA (crRNA) (Brouns et al., 2008; Carte et al., 2008; Deltcheva et al., 2011). The crRNA is used as a guide by Cas nucleases to find its complementary sequence, known as the protospacer, in the invading viral or plasmid genome (Gasiunas et al., 2012; Jinek et al., 2012; Jore et al., 2011; Samai et al., 2015). Target recognition through base-pairing between the crRNA and the target DNA results in the destruction of the invader and host immunity (Garneau et al., 2010).

Based on their cas genetic repertoire, CRISPR-Cas systems have been classified into six types, I through VI (Makarova et al., 2015; Shmakov et al., 2015). Cas9 is the crRNA-guided nuclease of the type II-A CRISPR-Cas system of Streptococcus pyogenes (Jinek et al., 2012). In addition to protospacer recognition by the crRNA, Cas9 target cleavage requires a 5′-NGG-3′ protospacer adjacent motif (PAM) immediately downstream of the target (Anders et al., 2014; Deveau et al., 2008; Jiang et al., 2013; Jinek et al., 2012). Cas9 is also required for the immunization step of the CRISPR response (Heler et al., 2015; Wei et al., 2015), using its PAM binding domain to specify functional spacer sequences that are flanked by the required NGG motif (Heler et al., 2015). In support of its role in spacer acquisition, Cas9 can associate in vivo with the other proteins encoded by the type II-A CRISPR-Cas system: Cas1, Cas2 and Csn2 (Heler et al., 2015). Cas9 systems have been utilized in a wide variety of compositions and methods, but there is an ongoing and unmet need for improvements in such systems, and methods of using them. This disclosure is pertinent to these needs.

SUMMARY

The present disclosure relates to a novel Cas9 enzyme comprising mutations that enhance its properties, relative to un-mutated Cas9. In particular, the altered Cas9 enzymes of this disclosure exhibit i) an increased rate of spacer acquisition, or ii) increased cleavage efficiency of targets with NAG PAMs, or a combination of i) and ii). The altered Cas9 enzymes comprise an amino acid substitution of 1473 and K500 in a Streptococcus pyogenes Cas9 enzyme, one non-limiting example of which is provided in SEQ ID NO:1 as a non-mutated sequence, but other homologous changes can be made in other Cas9 enzymes. Thus, in embodiments, novel Cas9 enzymes of this disclosure comprise sequences that are at least 80% similar to SEQ ID NO:1 across its length, but retain one or more of the increased rate of spacer acquisition, or increased cleavage efficiency.

The disclosure includes polynucleotides, including but not limited to expression vectors, that encode the Cas9 enzymes described herein, cells comprising such polynucleotides, and methods of using such cells for a variety of purposes, such as for use in labelling bacteria, and for enhancing phage acquired immunity in bacteria, such as those used in industrial processes, including but not necessarily limited to the food a beverage industry, such as the dairy industry.

The disclosure includes methods of making modified bacteria by introducing into them expression vectors that encode the novel Cas9 enzymes described herein, and includes the modified cells, their cell culture medium, cell lysates, and Cas9 enzymes isolated from the cells.

In one approach the disclosure provides a method comprising contacting bacteria that have been modified to express a Cas9 described herein with one or more bacteriophage such that at least one spacer sequence in the genome of the bacteriophage is acquired by the bacteria. Spacer acquisition is more efficient than compared to a reference, such as an unmodified Cas9, i.e., a Cas9 that does not contain the described mutations. In certain embodiments, the bacteria are contacted with a plurality of distinct bacteriophage, and the bacteria acquire a plurality of distinct spacer sequences. In such implementations, the bacteriophage can be obtained from any source, including but not limited to a bacterial culture that is used in connection with making or finishing a food or beverage product. Such food products made with the assistance of modified bacteria are included within this disclosure.

BRIEF DESCRIPTION OF FIGURES

Where color is described as a feature in the figures, arrows and text are also used to illustrate certain of those features.

FIG. 1. Directed evolution of cas9 generates mutants with increased specificity for NAG targets. See also FIG. 5. (A) Schematic diagram of the directed evolution assay. S. pyogenes cas9 was mutagenized by error-prone PCR and library amplicons were cloned into a plasmid carrying a spacer matching a TAG-adjacent target sequence on the ϕNM4γ4 phage. Library cells were infected with lytic phage to screen for mutants displaying improved NAG cleaving efficiency. (B) Phage propagation was measured as the number of plaque forming units (pfu) per ml of stock, on cells targeting the NAG-adjacent protospacer and harboring plasmids with different mutations on cas9: one of the “evolved” alleles or each of the six mutations present in this allele. Mutations with pfu values significantly different than wild type are highlighted (**, p-value <0.05 compared to wtCas9). (C) Colony forming units (cfu) obtained after phage infection of naïve cells (not programmed to target any viral sequence) harboring plasmids with different mutations in cas9. Mutations with cfu values significantly different than wild type are highlighted. (D) Location of residues 1473 and K500 on the Cas9:single-guide RNA ribonucleoprotein (PDB 4UN3). Red, 1473; purple, K500; orange, sgRNA; green, target DNA (the GG PAM highlighted in red); grey, alpha-helical (REC) lobe; yellow, HNH domain; light blue, RuvC domain; blue, PAM-interacting CTD.

FIG. 2. Cas9′³′, or hyper-Cas9 (hCas9) mounts an enhanced CRISPR adaptive immune response. See also FIG. 6. (A) Representative plates obtained after lytic infection of cells harboring the full CRISPR system of S. pyogenes with wtCas9 or hCas9, showing the number of surviving colonies. (B) Agarose gel electrophoresis of PCR products of the amplification of the CRISPR of arrays of surviving cells to detect newly acquired spacers (asterisks). Molecular markers (in kb) are indicated in black, number of new spacers added in green. (C) Quantification of total surviving colonies (gray bars) and surviving colonies with newly incorporated spacers, as detected by PCR (blue and red bars). Data are represented as mean±SEM of 3 representative biological replicates. (B) Growth curves of cultures of cells harboring the full CRISPR system of S. pyogenes with wtCas9 or hCas9, with (+) or without (−) phage infection. (E) PCR-based analysis of the liquid cultures shown in C (at 24 hours post-infection) to check for the acquisition of new spacer sequences in the presence (+) or the absence (−) of phage ϕNM4γ4 infection, by cells expressing wtCas9 or hCas9. Molecular markers (in kb) are indicated in black, number of new spacers added in green. Image is representative of three technical replicates.

FIG. 3. hCas9 has increased interference efficiency against NAG- but not NGG-adjacent targets. See also FIG. 7. (A) Growth curves of cultures infected with ϕNM4γ4 harboring the wtCas9 or hCas9 (but not Cas1, Cas2 and Csn2) programmed to target either NAG- or NGG-flanked viral sequences. (B) Phage propagation, measured in pfu/ml, of the bacteria presented in A. (C) Cleavage of radiolabeled dsDNA targets flanked by either NGG or NAG PAMs, by wtCas9 or hCas9. (D) Quantification of the cleavage results shown in C. Data are represented as mean SD of 3 representative biological replicates.

FIG. 4. hCas9 promotes higher rates of spacer acquisition. See also FIG. 8. (A) Schematic diagram of the S. pyogenes CRISPR locus showing the barcode and primers (arrows) used to measure the number of independent spacer acquisition events. (B) Cultures expressing wtCas9 or hCas9 were infected with ϕNM4γ4 phage, surviving cells were collected after 24 hours, DNA extracted and used as template for PCR of the CRISPR arrays. Amplification products were separated by agarose gel electrophoresis (not shown) and the DNA of the expanded CRISPR array was subject to MiSeq next-generation sequencing. The number of barcodes for each spacer sequence across the phage genome, normalized by the total number of spacer reads obtained, was plotted. (C) The hCas9/wtCas9 frequency of independent acquisition events ratio for 1938 common spacer sequences was plotted across the phage genome. The zone where the ratio is greater than one is shown in grey. The red line shows the average ratio. (D) Same as (B) but without phage infection; i.e. a measure of acquisition of spacers derived from the host chromosome and resident plasmids. (E) Pair-wise competition between staphylococci expressing wtCas9 or hCas9. The change in the relative frequency of cells carrying the hcas9 allele (y-axis) is plotted against the number of culture transfers (one transfer per day, x-axis).

FIG. 5. Protection of host cells by hCas9 programmed against different NAG-flanked targets. Related to FIG. 1. (A) The ability of hCas9 to target protospacers with different PAM was tested by measuring phage propagation in cells harboring CRISPR-Cas systems containing either wtCas9 or hCas9 and programmed to target the sequences shown, which are followed by TAG, AAG, GAG or CAG PAMs. The sequences listed in this figure are SEQ ID NO:128, SEQ ID NO:129, and SEQ ID NO:130. (B) Phage propagation was measured as the number of plaque forming units (pfu) per ml of stock, on cells targeting the TAG, AAG, GAG, and CAG-adjacent protospacers and hCas9. Data are represented as mean±SD of three representative biological replicates. (C) Measurement of pfu formation on staphylococci carrying plasmids with different cas9 mutations after infection with ϕ85, a phage lacking the target recognized in ϕNM4γ4. Data are represented as mean±SD of three representative biological replicates. (D) Location of residue K500 on the Cas9:single-guide RNA ribonucleoprotein (PDB 4UN3). Purple, K500; orange, sgRNA; green, target DNA (the GG PAM highlighted in red); grey, alpha-helical (REC) lobe; yellow, HNH domain; light blue, RuvC domain; blue, PAM-interacting CTD.

FIG. 6. CRISPR-Cas immune response of cells expressing Cas9^(1473A). Related to FIG. 2. Cultures harboring plasmids with tracrRNA, cas1, cas2 and csn2 genes, and either wild-type, I473F or I473A cas9 alleles, were infected with ΦNM4γ4 phage on top agar media and poured on plates. After 24 hours of incubation at 37° C. the CRISPR-surviving colonies were counted. Data are represented as mean±SD of three representative biological replicates.

FIG. 7. In vivo and in vitro targets. Related to FIG. 3. (A) Region of the ΦNM4γ4 phage genome (nucleotides 1441 to 1490) containing the TAG- and TGG-flanked protospacers, yellow and blue respectively, used in FIGS. 3A and 3B. This figure contains SEQ ID NO:131. (B) Sequences of the dsDNA target oligonucleotides used in FIG. 3C. The protospacer sequence is the same, but it is flanked by either a TAG (yellow) or TGG (blue) PAM sequence. Radiolabel is at the 5′ end (P). Grey and black arrowheads mark the cleavage sites of the RuvC and HNH domains, respectively. This figure contains SEQ ID NO:132, SEQ ID NO:133, SEQ ID NO:134, and SEQ ID NO:135.

FIG. 8. Analysis of next-generation sequencing results. Related to FIG. 4. (A) Data presented in FIG. 4B and in Supplementary Data File was plotted as the number of reads for each spacer sequence across the phage genome, normalized by the total number of spacer reads obtained. Spacers matching protospacers with NGG PAMs are shown in blue, with NAG PAMs in yellow. (B) Quantification of the data shown in panel A.

(C) Quantification of the data shown in FIG. 4B. (D) Alignment of Cas9 protein sequences belonging to type II CRISPR-Cas systems. Highlighted in orange is the 1473 residue. An equivalent residue is not found in some type II-B and II-C systems. This figure contains SEQ ID NO:136, SEQ ID NO:137, SEQ ID NO:138, SEQ ID NO:139, SEQ ID NO:140, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:152, SEQ ID NO:153, SEQ ID NO:154, and SEQ ID NO:155. (E) Fraction (%) of staphylococci retaining the plasmid harboring wtcas9 and hcas9 after 10 days of culture; with one transfer (1:100 dilution into fresh media) per day. Cells were plated in solid media with and without chloramphenicol, an antibiotic that selects for cells harboring the pCRISPR plasmid. The fraction of staphylococci carrying this plasmid was obtained dividing the chloramphenicol-resistant cfu by the total cfu count. Data are represented as mean±SD of three representative biological replicates.

FIG. 9. Patterns spacer acquisition from the virus ϕ12γ3 using hyper or wt cas9. a, Abundance (RPM_(ϕ12)) of ℠12γ3 sequences incorporated into the CRISPR array after a 30 minute infection at MOI 100 of cells harboring h cas9 (purple) or wt cas9 (green). b, Individual spacers common to both datasets in panel c were plotted with RPM_(ϕ12) values for h cas9 on the y-axis and wt cas9 on the x-axis. cos, cohesive end; chi, first chi site upstream of the cos site. The diagonal dotted line indicates the identity line.

DETAILED DESCRIPTION

Unless defined otherwise herein, all technical and scientific terms used in this disclosure have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure pertains.

Every numerical range given throughout this specification includes its upper and lower values, as well as every narrower numerical range that falls within it, as if such narrower numerical ranges were all expressly written herein.

The disclosure includes all polynucleotide sequences described herein, including RNA and DNA equivalents of each of the sequences, their complementary sequences, their reverse sequences, and the reverse complements of the sequences, and proteins encoded by the sequences, including polynucleotides encoding proteins described herein.

The present disclosure provides compositions and methods that relate in general to novel Cas9 enzymes, referred to herein as “hyper Cas9” and “hCas9”. The disclosure includes isolated Cas9 enzymes, cells comprising/expressing the novel Cas9 enzymes, including but not necessarily limited to populations of bacterial cells and their progeny, polynucleotide sequences and expression vectors encoding the novel Cas9 enzymes, kits comprising expression vectors encoding the novel Cas9 enzymes, and/or cells expression the novel Cas9 enzymes. Methods of making cells that express the novel Cas9 enzymes for numerous purposes are provided and are described further below. gRNAs and/or expression vectors/polynucleotides encoding them can optionally be included in compositions, kits and products of this disclosure. In embodiments, expression vectors can encode any suitable activating crRNA (tracrRNA) gene, or another expression vector can be included to express the crRNA.

The novel hCas9 enzymes of this disclosure are functionally and structurally distinct from their naturally occurring counterparts. Structurally hCas9 enzymes differ in amino acid sequence from wild type Cas9. Functionally, the hCas9 enzymes have at least one of the following properties relative to their wild type counterparts: i) increased rate of spacer acquisition, ii) increased cleavage efficiency of targets with NAG PAMs.

In embodiments, an hCas9 of this disclosure comprises a modified Streptococcus pyogenes hCas9. In embodiments, the modification comprises a substitution of at least one of the following amino acids: 1473 and K500. It is believed any substitution of these amino acids can be made, provided the modified Cas9 exhibits at least one of i) increased rate of spacer acquisition, and ii) increased cleavage efficiency of targets with NAG PAMs. In embodiments, conservative amino substitutions are made. In certain embodiments the amino acid changes comprise at least one of I473F, I473A and K5001. These amino acids have positions according to the known reference sequence of S. pyogenes, which is available under GenBank accession no. NC 002737, with the cas9 gene at position 854757-858863. The S. pyogenes Cas9 amino acid sequence is available under number is NP_269215. These sequences are incorporated herein by reference as they were provided in the database on the priority date of this application or patent. In embodiments, the disclosure encompasses making the same or similar amino acid changes in Cas9 enzymes that are from bacteria other than S. pyogenes, including but not necessarily limited to S. aureus Cas9. In an embodiment, the mutations are present in a Cas9 amino acid sequence that comprises between 80-99% similarity to the following sequence, so long as the modified Cas9 includes at least one of the properties described above, e.g., i) increased rate of spacer acquisition, and ii) increased cleavage efficiency of targets with NAG PAMs:

(SEQ ID NO: 1) 1 mdkkysigld igtnsvgwav itdeykvpsk kfkvlgntdr hsikknliga llfdsgetae 61 atrlkrtarr rytrrknric ylqeifsnem akvddsffhr leesflveed kkherhpifg 121 nivdevayhe kyptiyhlrk klvdstdkad lrliylalah mikfrghfli egdlnpdnsd 181 vdklfiqlvq tynqlfeenp inasgvdaka ilsarlsksr rlenliaqlp gekknglfgn 241 lialslgltp nfksnfdlae daklqlskdt ydddldnlla qigdqyadlf laaknlsdai 301 llsdilrvnt eitkaplsas mikrydehhq dltllkalvr qqlpekykei ffdqskngya 361 gyidggasqe efykfikpil ekmdgteell vklnredllr kqrtfdngsi phqihlgelh 421

481

541 sgeqkkaivd llfktnrkvt vkqlkedyfk kiecfdsvei sgvedrfnas lgtyhdllki 601 ikdkdfldne enedilediv ltltlfedre mieerlktya hlfddkvmkq lkrrrytgwg 661 rlsrklingi rdkqsgktil dflksdgfan rnfmqlihdd sltfkediqk aqvsgqgdsl 721 hehianlags paikkgilqt vkvvdelvkv mgrhkpeniv iemarenqtt qkgqknsrer 781 mkrieegike lgsqilkehp ventqlqnek lylyylqngr dmyvdqeldi nrlsdydvdh 841 ivpqsflkdd sidnkvltrs dknrgksdnv pseevvkkmk nywrqllnak litqrkfdnl 901 tkaergglse ldkagfikrq lvetrqitkh vaqildsrmn tkydendkli revkvitlks 961 klvsdfrkdf qfykvreinn yhhandayln avvgtalikk ypklesefvy gdykvydvrk 1021 miakseqeig katakyffys nimnffktei tlangeirkr plietngetg eivwdkgrdf 1081 atvrkvlsmp qvnivkktev qtggfskesi lpkrnsdkli arkkdwdpkk yggfdsptva 1141 ysvlvvakve kgkskklksv kellgitime rssfeknpid fleakgykev kkdliiklpk 1201 yslfelengr krmlasagel qkgnelalps kyvnflylas hyeklkgspe dneqkqlfve 1261 qhkhyldeii eqisefskry iladanldkv lsaynkhrdk pireqaenii hlftltnlga 1321 paafkyfdtt idrkrytstk evldatlihq sitglyetri dlsqlggd 

The disclosure includes methods for using the novel Cas9 enzymes for a wide variety of purposes, including but not necessarily limited to increasing frequency of CRISPR spacer acquisition, labeling cells that have been modified by spacer acquisition, detecting cells that have been labeled accordingly, the labeled cells themselves, and increasing the efficiency of CRISPR target editing. In embodiments the disclosure comprises improved approaches to Cas9/CRISPR immunization of populations of bacteria against infection by one or more distinct types of bacteriophages. Thus, it is expected that any Cas9-implemented method or approach, whether now known or hereafter developed, will benefit from including a novel Cas9 of this disclosure. The disclosure also includes a wide variety of products, including but not necessarily limited to cell products and food products that have been directly or indirectly exposed to a novel Cas9 of this disclosure, or to bacteria that express such a Cas9. In this regard, the disclosures of U.S. patent publication no. 20150093473, U.S.

patent publication no. 20130158245, and U.S. Pat. Nos. 7,919,277, 8,361,725, and 9,399,801 are incorporated herein by reference. In embodiments, a novel Cas9 enzyme of this disclosure is used as a substitute for, or in addition to, any CRISPR-based system and/or CRISPR based methods disclosed in any of these patent publications and patents.

In certain approaches the disclosure comprises modified bacteria that express a novel Cas9 enzyme of this disclosure. In embodiments, the disclosure includes modified gram negative bacteria that expresses a novel Cas9 enzyme. In embodiments, the disclosure includes modified bacteria that are facultative anaerobes. In embodiments the modified bacteria are gram positive bacteria that expresses a novel Cas9 enzyme of this disclosure. In embodiments the gram positive bacteria are members the Lactobacillus genus, and in particular Lactobacillus species that are active in the production of food products intended for human and/or non-human animal consumption. In non-limiting embodiments the modified bacteria are Lactobacillus species that are active in the production of dairy products, such as yogurt, milk, milk-based creams, ice cream products, and cheese, or fermented drinks, such as wine, cider and beer, or fermented foods, or combinations of the foregoing. In certain embodiments the modified bacteria are L. plantarum, L. casei, L. acidophilus, L. salivarius, or L. reuteri as well as probiotic strains of Bifidobacterium (i.e. B. longum).

In embodiments the disclosure includes combinations of modified bacteria described herein, and further comprises combinations of the modified bacteria with other microorganisms, such as yeasts. Those skilled in the art will recognize that such combinations are useful for production of certain foods.

In another aspect the disclosure comprises a food product comprising a modified bacteria that expresses a novel Cas9 enzyme of this disclosure. Such products include all of the aforementioned types of food and modified bacteria. In embodiments the food product is a dairy product, including but not necessarily limited to yogurt, milk, milk-based creams, and cheese. Use of microorganisms in making foods that intentionally contain live cultures, such as yogurts, are well known in the art and can be adapted for use with the presently provided modified microorganisms. In embodiments the food product is intended to, is undergoing, or has undergone a fermentation process. In one aspect the food product is a non-human animal feed.

In certain aspects the disclosure provides a product, such as a food product, which comprises packaging, such as a paper or cardboard carton, a plastic container, bottle, bag, etc., that are typically used for containing foods. The packaging can provide printed material, which includes information that identifies the modified bacteria present in the food product. Bacterial culture containers with such labels are also included in products and kits of this disclosure.

In another aspect the disclosure includes a supplement product, such as a nutraceutical product, a dietary supplement, a food ingredient, etc., including but not limited to a probiotic formulation or functional food that contains one or more live modified bacteria as described herein. The supplement product can be provided in the form of, for example, a liquid, capsules, tablets, softgels, powders, freeze-dried compositions, and the like. These products can have similar labeling as discussed above.

In an embodiment the disclosure includes making modified bacteria that express a novel Cas9 enzyme for use in a variety of purposes, including but not limited to inhibiting bacteriophage infections. The method comprises introducing into bacteria a heterologous DNA sequence encoding a novel Cas9 enzyme, and culturing the bacteria for use in, on or during production of any product described herein or as would otherwise be apparent to one skilled in the art given the benefit of this disclosure, including but not necessarily limited to food and beverage products, and as a probiotics, or nutraceuticals. In embodiments, the bacteria are bacteria used in any industrial application, including but not necessarily limited to biofuel production, petroleum spill cleanup, as well as in the production of cosmetics, pharmaceuticals and construction materials.

In embodiments, the disclosure comprises modified bacterial cultures themselves. In embodiments, the cultures are propagated as, for example, a yogurt culture. In certain embodiments, the disclosure provides a bacteria starter culture that comprises a novel Cas9 enzyme of this disclosure, and may include progeny of such a starter culture, even if the progeny do not maintain the Cas9 enzyme or an expression vector encoding it.

Bacteria modified according to this disclosure can comprise any suitable expression vector that encodes a novel Cas9 enzyme described herein. Such expression vectors can comprise typical components, such as cloning sites, selectable markers, origins or replication, promoters, expression/secretion signals, purification signals, etc. Commercially available vectors can be adapted to express the novel Cas9 enzymes. In embodiments, the disclosure includes use of a tracrRNA. The tracrRNA can comprise a segment that is complementary to a pre-crRNA, such that a portion of the tracrRNA and pre-crRNA can form an RNA duplex. The RNA duplex is cleaved by RNase III, resulting in the formation of a crRNA/tracrRNA hybrid complex. This hybrid functions as a guide for Cas, which cleaves a target sequence. In general, a tracrRNA used in embodiments of the present disclosure will comprise or consist of from 40 to 200 nucleotides, inclusive, and including all integers and ranges there between. There are a wide variety of publicly available resources that can be used to design suitable tracrRNA sequences and such tracrRNA sequences can be adapted for use with embodiments of the present disclosure. In general a mature crRNA, meaning a crRNA that is complexed with a Cas9 enzyme during cleavage of a DNA target sequence, will comprise or consist of from 20-60 nucleotides. In embodiments, a crRNA comprises or consists of 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nt of the spacer (targeting) sequence followed by 19-22 nt of repeat sequence.

In one approach the disclosure comprises introducing into bacteria an expression vector encoding a novel Cas9 enzyme of this disclosure, wherein the bacteria exhibit increased spacer acquisition relative to a suitable control, and/or exhibit inhibition of phage propagation in an amount greater than a suitable control. The control can be, for example, the rate of spacer acquisition and/or inhibition of phage propagation achieved by bacteria expressing a wild type Cas9 enzyme, or a modified Cas9 enzyme that does not comprise at least one of I473F or K5001 mutations described herein. In this regard, we demonstrate in this disclosure that Cas9 mutants comprising other mutations, such as R425G, S701G, P756L and A1032G, show wild-type levels of phage propagation and therefore do not contribute to the gain-of-function-phenotype of the cas9 alleles that are subjects of this disclosure. Notably, modified bacteria comprising Cas9 with the I473F or K5001 mutations decrease phage propagation by about four orders of magnitude. We also demonstrate enhanced phage immunity against NGG-flanked targets as well as other NAG PAMs, such as AAG, CAG, and GAG. Thus, it will be recognized that the I473F and K500I mutations enhance the ability of Cas9 to recognize targets with NAG flanking PAMs and are broadly applicable to spacer acquisition and inhibition of a wide spectrum of bacteriophage types.

In one embodiment, the disclosure comprises separating a plurality of bacteriophage from a bacteria population, wherein the bacteria population may comprise bacteria that either do not express a Cas9 enzyme, or express a Cas9 enzyme that is distinct from a novel Cas9 enzyme of this disclosure. The separated phage can be used directly, or isolated and purified to any desired degree of purity, processed, propagated and/or otherwise processed, and then used to infect a population of bacteria that express a novel Cas9 enzyme of this disclosure. Due to the increased spacer acquisition capabilities of these modified bacteria, it is expected that they will become immunized against a plurality of the phage more efficiently than bacteria that express an unmodified Cas9. In certain embodiments, the modified bacteria may become immunized against a broader diversity of phage as compared to bacteria that express an unmodified Cas9. In an embodiment, the disclosure comprises culturing the immunized bacteria to provide an immunized bacteria population. In certain implementations, the immunized bacteria comprise a starter culture for use production of any product described herein. In embodiments, the starter culture is used for the production of dairy products that are otherwise susceptible to phage infection. In embodiments, the disclosure provides bacteria cultures that comprise bacteria that are resistant to phage infection. In embodiments, the cultures can comprise from 10%-100% phage-resistant bacteria, wherein such resistance can be against a single phage type (i.e., homogenous phage genomes), or against distinct phage types (i.e., heterogeneous phage genomes).

In analyzing the role of Cas9 in spacer acquisition, we analyzed its PAM specificity. We tested in vivo cleavage of targets having the same protospacer sequence but different PAMs displaying all possible trinucleotide combinations (Jiang et al., 2013). We found that, in addition to the complete cleavage of targets with NGG PAMs, wild-type Cas9 displays approximately 50% of in vivo cleavage of targets with NAG PAMs. In an effort to understand how Cas9 affects the acquisition of spacers flanked by NGG motifs, we evolved this weak but detectable affinity of the nuclease for NAG PAMs. After structural analysis determined the PAM interacting domain of Cas9 (Anders et al., 2014; Jinek et al., 2014), different groups have specifically mutated this domain to obtain a versatile set of nucleases for genome editing purposes and have obtained an NAG-recognizing Cas9 (Kleinstiver et al., 2015b). In the present disclosure we took a different approach and searched for mutations in any region of the nuclease that would increase its specificity for NAG-flanked targets. We found one such mutation, I473F, which provided partial immunity when Cas9 was programmed to recognize an NAG viral protospacer; i.e. loaded with the complementary crRNA guide. This mutation also expanded the levels of the CRISPR-Cas adaptive immune response, increasing the number of CRISPR-mediated, bacteriophage-resistant colonies by more than two orders of magnitude. We performed experiments to understand the molecular basis of the enhanced CRISPR-Cas immunity and determined that the I473F mutation mediates a significant increase in spacer acquisition. Our results highlight the role of Cas9 during CRISPR immunization and provide a useful tool to study this otherwise rare process, as well as for use in the compositions and methods described above.

The following examples are presented to illustrate the present disclosure. They are not intended to be limiting in any manner. In some aspects, these Examples include routine techniques and methods used in the field of genetic engineering and molecular biology that are not otherwise described. The following resources include descriptions of general methodology useful in accordance with the invention: Sambrook et al., Molecular Cloning: A Laboratory Manual (4th Ed., 2012); Kreigler, Gene Transfer and Expression: A Laboratory Manual (1993) and Ausubel et al., Eds. Current Protocols in Molecular Biology (1995). These general references provide definitions and methods known to those in the art. However, it is not intended that the present disclosures be limited to any particular methods, protocols, and reagents described, as these may vary in ways that will be understood by the skilled artisan. Hypothesis described herein are not intended to constrain the disclosure to any particular theory.

Example 1

Directed Evolution of Cas9 Yields a Mutant with Altered PAM Specificity and Enhanced CRISPR-Cas Immunity.

S. pyogenes Cas9 has an innate ability to cleave NAG-adjacent targets, but with much lower efficiency than it cleaves canonical (NGG) targets (Jiang et al., 2013). To improve its specificity for NAG PAMs, we constructed a library of plasmids carrying cas9 variants generated by error-prone PCR (FIG. 1A). The library plasmids also harbor the trans-activating crRNA (tracrRNA) gene (Deltcheva et al., 2011) and a single-spacer CRISPR array targeting a TAG-adjacent protospacer on the genome of the lytic staphylococcal bacteriophage ϕNM4γ4 (Goldberg et al., 2014). The library was transformed into Staphylococcus aureus RN4220 cells that were subjected to two rounds of phage infection on soft-agar plates to select for phage-resistant bacterial colonies. Several colonies were obtained and we proceeded with a more extensive analysis of one of the “evolved” mutants that gained phage resistance. Sequencing of the plasmid revealed the presence of six single-nucleotide substitutions in the cas9 gene (see Extended Experimental Procedures) producing the following missense mutations: R425G, I473F, K500I, S701G, P756L and A1032G. To evaluate the importance of each of these mutations in the gain-of-function phenotype we introduced them individually into the cas9 gene and tested the ability of the resulting plasmid to prevent ϕNM4γ4 propagation by measuring the number of plaque forming units (pfu) that result after infection of the host cells (FIG. 1B). Cas9 harboring the R425G, S701G, P756L and A1032G mutations allow wild-type levels of phage propagation and therefore do not contribute to the gain-of-function-phenotype of the evolved cas9 allele we isolated. In contrast, cells containing Cas9 with the I473F or K5001 mutations decrease phage propagation by about four orders of magnitude. This is close to the levels of immunity provided by wild-type Cas9 when programmed against NGG-flanked targets (a reduction of 5 orders of magnitude, see FIG. 3B). Similar results were obtained when other NAG PAMs were tested (AAG, CAG, GAG, FIGS. 5A-B). Therefore the I473F and K5001 mutations enhance the ability of Cas9 to recognize targets with NAG PAMs. The pfu count was similar in all mutant and control strains when infected with ϕ85, a lytic phage that lacks the target sequence (FIG. 5C), corroborating that the decrease in phage propagation observed for the I473F and K5001 mutations is a direct consequence of Cas9 targeting and not due to cell toxicity induced by the various mutants.

Given the requirement of Cas9 for the immunization phase of the CRISPR-Cas immune response, i.e. the acquisition of virus-derived spacer sequences (Heler et al., 2015; Wei et al., 2015), we wondered whether the evolved Cas9 as well as the individual mutants affected this process. To test this, we introduced the different alleles of cas9 into a plasmid harboring the tracrRNA gene, the S. pyogenes SF370 CRISPR array (containing six spacers, none of them matching the genome of ϕNM4γ4) and the type II-A genes exclusively involved in the acquisition of new spacers, cas1, cas2 and csn2 (Heler et al., 2015; Wei et al., 2015). S. aureus cells containing the different plasmids were infected with ϕNM4γ4 and the number of survivors were enumerated as colony forming units (cfu) (FIG. 1C). Only a small fraction of cells containing wild-type Cas9 are able to acquire new spacers, about 2-fold over a CRISPR-less control. In contrast, the evolved cas9 allele containing all six mutations increased the number of CRISPR-surviving cells by about 60-fold. Analysis of single mutants revealed that this highly significant increase was provided almost exclusively by the I473F mutation (FIG. 1C). Due to the sharp enhancement of the CRISPR-Cas immune response conferred by the I473F mutation we decided to name the Cas9^(1437F) mutant “hyper-Cas9”, or hCas9. 1473 is located close to the surface of Cas9, outside of the PAM-interacting domain, and it is part of a projection from the Helical III domain that interacts with the nexus of the guide RNA (Jiang et al., 2016) (FIG. 1D). This position does not suggest an evident effect of the I473F mutation on Cas9 activity and therefore we decided to investigate the basis for its phenotype by performing a detailed comparison with the CRISPR-Cas immune response mediated by wild-type Cas9.

Example 2

hCas9 Enhances the CRISPR-Cas Adaptive Immune Response by Two Orders of Magnitude.

To perform a more accurate comparison between wild-type (wtCas9) and hCas9, we counted the number of CRISPR-mediated, phage resistant cells that arise after phage infection. FIG. 2A shows representative plates of infected cells containing plasmids with the wtCas9 or hCas9 S. pyogenes CRISPR-Cas locus, showing a striking difference in the number of surviving colonies. Most of these colonies arise from single cells that were able to acquire a new spacer matching the ϕNM4γ4 genome. However, a fraction of the surviving cells repel phage attack by non-CRISPR related mechanisms, such as envelope resistance (Heler et al., 2015). To make a more accurate quantification of the CRISPR-Cas response, we analyzed individual colonies by PCR of the CRISPR array (Heler et al., 2015; Yosef et al., 2012) to detect those in which new spacers were acquired, i.e. “adapted” cells (FIG. 2B). Not only did many more resistant colonies originated from cells harboring hCas9 (an average of 31 cfu for wtCas9 vs 4,312 cfu for hCas9, FIG. 2C), but also most of them showed CRISPR-mediated phage resistance (23% for wtCas9 vs 90% for hCas9, FIG. 2C). We wondered whether this was a consequence of the specific substitution of 1473 by phenylalanine. To test this we introduced an I473A mutation into Cas9 (FIG. 7). We found that cells harboring the I473A mutant produced a number of CRISPR-mediated immune cfu comparable to cells carrying wtCas9, but 10 times lower than the cfu obtained from infection of cells expressing hCas9. Therefore we conclude that the I473F mutation increases the CRISPR-adaptive immune response through a specific effect of the phenylalanine residue in position 473 and by more than two orders of magnitude: on average, approximately 7 cfu (31×0.23) per experiment for infected wtCas9-containing cells, and approximately 3,863 cfu (4,312×0.90) for infected hCas9-expressing bacteria. We sequenced PCR products to determine the PAM of the spacers acquired by 40 colonies expressing wtCas9 (Table 1) or hCas9 (Table 2). Interestingly, all 40 spacers acquired by cells expressing hCas9 matched targets with an NGG PAM, suggesting that this nuclease can still target sequences followed by the canonical PAM in addition to targets with NAG PAMs.

Similar results were observed when cells in culture carrying naïve wtCas9 or hCas9 CRISPR-Cas systems were infected with phage. Upon addition of ϕNM4γ4, the cultures lyse, as the vast majority of cells do not undergo spacer acquisition (FIG. 2D). Nonetheless, hCas9 cultures were able to regrow much earlier (˜14 hours post-infection) than wtCas9 cultures (-17 hours post-infection). PCR analysis using DNA extracted from the whole culture at 24 hours post-infection corroborated the earlier observation that hCas9 cells mount a more robust CRISPR immune response (FIG. 2E). Whereas the PCR products derived from wtCas9 staphylococci showed the presence of both adapted and non-adapted CRISPR arrays in the surviving population, the PCR results from cultures carrying hCas9 showed very little non-adapted CRISPR arrays, with the great majority of the cells acquiring one or two new spacers. Altogether these data show that the I473F mutation in Cas9 allows for a more robust CRISPR-Cas immune response due to a specific effect of the phenylalanine residue.

Example 3

hCas9 Displays a Modest Increase in the Cleavage Efficiency of Targets with NAG PAMs.

Next, we analyzed whether the enhanced immunity phenotype of hCas9 documented in FIG. 2 was due to an increase in the frequency of spacer acquisition, a more robust cleavage by hCas9 of its targets, or both. First we considered the possibility that hCas9 could provide better cleavage of the infecting viral DNA. In this scenario both wtCas9 and hCas9 populations can acquire a similar number of new spacers but a more robust cleavage of the target DNA by hCas9 would lead to a faster recovery of the bacteria that acquired the spacers. To test this hypothesis, we infected cells carrying plasmids with either wtCas9 or hCas9 programmed to target the ϕNM4γ4 virus and the tracrRNA gene, but without the spacer acquisition machinery (cas1, cas2 and csn2). This genetic background supports CRISPR-Cas anti-viral defense but does not allow the acquisition of new spacer sequences (Heler et al., 2015). Because our data suggested that hCas9 can still target protospacers followed by NGG PAMs, we tested the immunity of cells programmed to attack targets with either an NAG or an NGG PAM located in the same region of the ϕNM4γ4 genome (FIG. 8A). Bacteria containing different plasmids were infected with phage during exponential growth and the optical density of the culture was followed over time to measure the immunity provided by Cas9 cleavage of the viral genome (FIG. 3A). As expected, cells harboring a vector control were rapidly lysed by the addition of phage. On the other hand, cells expressing wtCas9 or hCas9 programmed against an NGG target cleared the infection efficiently and continued the exponential growth, indicating that the I473F mutation does not affect the recognition and targeting of NGG-flanked sequences. In contrast, both cultures display poor survival when NAG-flanked protospacers were targeted by either Cas9 version, with cells expressing wtCas9 suffering a more substantial lysis than cells expressing hCas9. Similar results were obtained when we tested the same cultures for their ability to limit phage propagation (pfu/ml) (FIG. 3B).

Both in vivo experiments measuring bacterial survival (FIG. 3A) and phage propagation (FIG. 3B) suggest that hCas9 has not improved efficiency of cleavage of NGG-flanked targets, and displays only a small increase in the cleavage of NAG-flanked sequences. To unequivocally demonstrate this, we performed in vitro cleavage assays with purified wtCas9 and hCas9 (FIG. 3C). In this case, we were able to compare cleavage of radiolabeled oligonucleotides containing the same protospacer sequence followed by either a TGG or TAG PAM (FIG. 7B). Consistent with in vivo data, experiments showed similar cutting rates of the NGG target for wtCas9 and hCas9. Quantification of the cleavage products showed that hCas9 cleaved more of the NAG target than wtCas9 over longer timescales (FIG. 3D). Altogether, the data presented in FIG. 3 indicate that while there is a modest increase in the NAG-targeting properties of hCas9, this cannot explain the rise in the number of CRISPR-resistant colonies mediated by the I473F mutation (FIG. 2C).

Example 4

hCas9 Promotes Higher Rates of Spacer Acquisition.

A second hypothesis that could explain the increase in CRISPR-Cas immunity conferred by hCas9 is an increase in the frequency of spacer acquisition by the cells expressing this mutant. To test this we performed a comparison of the spacer repertoires acquired by cells harboring wtCas9 or hCas9. We made two plasmid libraries, carrying the spacer acquisition genes cas1, cas2 and csn2 and wtcas9 or hcas9, the tracrRNA gene and the S. pyogenes CRISPR array preceded by a “barcode” sequence of 10 nucleotides 50 bp immediately upstream of the CRISPR array (FIG. 4A). Cells harboring each library were infected with phage ϕNM4γ4 and DNA from the surviving cells was used to amplify the CRISPR array via PCR and collect sequence information of all the new acquired spacers using next generation sequencing. The primers used also amplify the barcode sequence (FIG. 4A) and therefore each new spacer sequence can be associated with a unique barcode, allowing us to count how many times a given spacer was independently acquired in each bacterial population. Over three million reads belonging to either library were analyzed. The frequency of reads corresponding to each acquired spacer sequence was plotted according to its position in the ϕNM4γ4 genome (FIG. 8A). Analysis of the PAMs of the acquired spacers showed that over 99.5% of the spacers matched NGG targets in both libraries (FIG. 8B), corroborating our in vivo data showing that hCas9 retained NGG PAM specificity. In addition, we looked at the repertoire of unique different spacers independently of the number of reads per sequence (FIG. 8C). Consistent with our previous finding that the PAM specificity of Cas9 is responsible for the PAM sequence of the new protospacers, the hCas9 library showed a 5-fold increase in the acquisition of spacers matching NAG-flanked targets. Even with this increase these spacers represent less than 0.05% of the total acquisition events, most likely due to the fitness cost associated with the low efficiency of NAG-target cleavage observed for hCas9 when compared with its cleavage of NGG targets. We also observed an increase in the total number of different spacer sequences, from 1980 for wtCas9 cells to 2500 for the hCas9 sample. All together, these findings show that hCas9 provides the host bacterium with highly efficient spacer acquisition, thus enhancing CRISPR-Cas immunity.

To calculate the frequency of acquisition of every spacer we divided the number of different barcodes for a given spacer sequence by the total number of reads. This value was plotted according to its position in the ϕNM4γ4 genome (FIG. 4B). The data show a drastic increase in the frequency of acquisition in hCas9 cells. For all 1938 newly acquired spacer sequences shared between the two libraries, we calculated the ratio of unique adaptation events (i.e. number of different barcodes) for hCas9 reads compared to wtCas9 (FIG. 4C). We found that more than 97% of the spacers were acquired more frequently in the hCas9 library (ratio >1), with an average ratio of −18. This experiment indicates that hCas9 enhances the rate of spacer acquisition during the CRISPR adaptation phase. To rule out any effect that the phage selection imposed on adapted cells could have on our experiments we looked at the rates of spacer acquisition in the absence of phage infection. Using our barcoded system, we passaged cells expressing wtCas9 or hCas9 for 10 days, and subjected a PCR product containing the CRISPR locus of each culture to next generation sequencing.

The frequency of acquisition was one order of magnitude higher for hCas9-expressing cells (FIG. 4D). Altogether, these findings show that hCas9 provides the host bacterium with more efficient spacer acquisition, and suggest that this is a major contributor to the enhanced CRISPR-Cas immunity granted by hCas9.

Higher levels of immunization during the CRISPR-Cas response to phage infection provides better host defense. However, this could also lead to detrimental effects in the absence of infection, leading to high levels of CRISPR “autoimmunity”. Consistent with this scenario, the I473F mutation was not found in type II-A cas9 gene variants (FIG. 8D). To explore the possible detrimental effects of hCas9 we looked at the rates of plasmid loss in the absence of phage infection since in our barcoded experiment without viral infection, as well in other similar experiments (Heler et al., 2015; Levy et al., 2015; Yosef et al., 2012), most of the acquired self-spacers match plasmid sequences. To test this we plated cells after 10 days of growth with and without chloramphenicol to calculate the frequency of plasmid loss as the number of chloramphenicol-resistant cfu relative to the total cfu count (FIG. 8E). Whereas most staphylococci expressing wtCas9 maintained the plasmid, about 30% of the cells producing hCas9 lost it. This decrease was dependent on the presence of an active Cas1-Cas2 spacer integrase, demonstrating that plasmid loss was caused by CRISPR autoimmunity. Higher autoimmunity in hCas9-expressing cells resulted in a fitness cost, as shown by pairwise competition assays in which wtCas9- and hCas9-expressing cells were grown together and the relative proportion of each strain was measured over time (staphylococci harboring the hcas9, but not the wtcas9, plasmid also carried an erythromycin-resistance gene in their chromosome). We detected a decrease in the proportion of erythromycin-resistant cfu over time (FIG. 4E), demonstrating that a “hyper-acquiring” type II CRISPR-Cas system confers a fitness cost to the cells that carry it.

It will be apparent from the foregoing that this disclosure provides non-limiting demonstrations of random mutagenesis on the entire cas9 gene and which lead to the identification of a mutant with an expanded CRISPR-Cas response. This “hyper” Cas9 version (hCas9) harbors the mutation I473F. Compared to wild-type staphylococci, cells harboring hcas9 displays a modest increase in NAG-target recognition but a substantial increase (more than two orders of magnitude) in the frequency of spacer acquisition. The molecular mechanism by which the I473F mutation enables this increase in spacer acquisition is not clear. Without intending to be constrained by any particular theory, it is considered that, given its location on the surface of hCas9, F473 could interact with other Cas proteins and increase the abundance or the stability of the complex, thus enhancing the rate of spacer acquisition. To test this we incubated the four proteins along with a single-guide RNA (Jinek et al., 2012) and subjected them to gel filtration to detect the formation of the complex. However, we did not observe significant amounts of stable complexes neither in the presence of wtCas9 nor hCas9. In wtCas9, the isoleucine residue is in direct contact with bases of the tracrRNA (FIG. 1D) that are equivalent to the nexus in the single-guide RNA (Briner et al., 2014). Specifically, nucleotide U59 of the tracrRNA inserts into a hydrophobic pocket lined by 1473 and its adjacent residues (Jiang et al., 2016). It is possible that the bulkier phenylalanine residue could interfere with the tracrRNA:Cas9 association, affecting the involvement of Cas9 in the immunization step of the CRISPR-Cas response. This hypothesis is supported by the wild-type phenotype of the I473A mutation (FIG. 6), since the smaller alanine residue most likely will not interfere with the tracrRNA interaction. Another mutation in a residue close to 1473, K500I, also seems to affect Cas9 target specificity, but not the rate of spacer acquisition. K500 is located in the minor groove of the PAM-distal crRNA-target DNA duplex (FIG. 5D), near the backbone of nucleotide 12 of the DNA protospacer and nucleotide 3 of the crRNA (Anders et al., 2014). The loss of a basic residue in this region might alter target binding and recognition, analogous to the increase in specificity resulting from mutations of other residues making nonspecific DNA contacts (Kleinstiver et al., 2016).

In spite of the enhanced immune response provided by the I473F substitution, we could not find cas9 genes harboring this mutation in the genome of bacteria sequenced so far. Two studies have shown that Cas9 is required for the acquisition of self-targeting spacers (Heler et al., 2015; Wei et al., 2015), a situation that leads to “auto-immunity” and to the death of the host (Bikard et al., 2014; Jiang et al., 2013). Here we show that the enhanced rate of spacer acquisition of hCas9 results in an increase in the autoimmunity events and therefore leads to a fitness cost for the host cell. We believe that this prevents the evolution of the I473F mutation into Cas9.

The phenotype of the I473F mutation in Cas9 further demonstrates the involvement of this nuclease in the acquisition of new spacers in type II CRISPR-Cas systems and provides a new tool that could facilitate the study of CRISPR immunization, making this process more frequent and easier to detect. In addition, hCas9 provides a useful tool for the development of technologies that use the incorporation of spacers to develop synthetic biology devices that can record different cellular events (Shipman et al., 2016). Currently, the low adaptation frequency limits the number of stimuli that can be captured as new spacers in the CRISPR array. Using an enhanced CRISPR adaptation machinery such as hCas9 could boost the spacer acquisition frequency and thus facilitate the development of this and other related synthetic biology technologies.

Example 5

This Example provides a description of the materials and methods used to obtain the results discussed above for FIGS. 1-4.

Bacterial Strains and Growth Conditions

Cultivation of S. aureus RN4220 (Kreiswirth et al., 1983) was carried out in heart infusion broth (BHI) at 37° C. Whenever applicable, media were supplemented with chloramphenicol at 10 μg ml⁻¹ to ensure pC194-derived plasmid maintenance or 5 mM CaCl₂ for phage adsorption.

Directed Evolution of Cas9

The cas9 gene was mutagenized at a low rate of 0-4.5 mutations/kb by error prone PCR using GeneMorph II Random Mutagenesis Kit. The mutant cas9 amplicons were cloned into a backbone plasmid containing a spacer matching a TAG-adjacent target on ϕNM4γ4. The library was subjected to soft-agar lytic phage infection and surviving colonies were re-streaked on fresh plates. The TAG-cleaving efficiency of surviving colonies was individually assessed by phage propagation assays.

High-Throughput Sequencing

Plasmid DNA was extracted from adapted cultures using the in-liquid spacer acquisition assay described in Experimental Procedures. 200 ng of plasmid DNA was used as template for Phusion PCR to amplify the CRISPR locus with primer pairs H372-H373 and H376-H377 (Table 3) for the wtcas9 and hcas9 libraries, respectively. Following gel extraction and purification of the adapted bands, samples were subject to Illumina MiSeq sequencing. Data analysis was performed in Python: first, all newly acquired spacer sequences were extracted from raw MiSeq FASTA data files. Next, the frequency (number of different barcode sequences), the phage target location and the flanking PAM were determined for each unique spacer sequence.

REFERENCES FOR THE FOREGOING DESCRIPTION

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Example 6

This Example Provides a Description of Experimental Procedures Used to Produce that Data Shown in FIGS. 5-8.

Spacer Acquisition Assay During Phage Infection

Spacer acquisition assays of cells harboring the full CRISPR system of Streptococcus pyogenes were performed as described previously, both in liquid and on plate (Heler et al., 2015). For plate acquisition assays, overnight cultures were launched from single colonies and diluted to equal optical densities. CRISPR arrays were amplified by PCR with primer pairs L400-H050 or L400-H052 (Table 3).

Spacer Acquisition Assay in the Absence of Phage Infection

Spacer acquisition assays were conducted by passaging cultures carrying the full S. pyogenes CRISPR system (expressing wtCas9 or hCas9) in the absence of phage for 10 days. Each day, the cultures were diluted 1:100 in fresh media with appropriate antibiotics. The pCRISPR plasmids had barcoded leader sequences. Spacer acquisition was quantified by PCR amplification of the CRISPR array followed by NGS.

Phage Propagation Assay

Overnight cultures were launched from single colonies. Serial dilutions of a stock of phage ϕNM4γ4 (Goldberg et al., 2014) or ϕ85 (Mazmanian et al., 2000) were spotted on fresh soft heart infusion agar (HIA) lawns of targeting cells containing chloramphenicol 10 μg m1⁻¹ and 5 mM CaCl₂. Plates were incubated at 37° C. overnight and interference efficiency was measured in plaque forming units (pfu).

Bacterial Growth Curves

Overnight cultures were launched from single colonies and diluted 1:100 in BHI. After 1 hour of growth, optical density at 600 nm (0D600) was measured for each culture, and samples were brought to equal cell densities and loaded into 96-well plates along with ϕNM4γ4 at MOI=1. Measurements were taken every 10 minutes for 24 hours.

Cas9 Target Cleavage Assay

Cas9 was expressed and purified as previously described (Jinek et al., 2012). The I473F Cas9 expression vector was cloned by around-the-horn mutagenic PCR (Moore and Prevelige, 2002). crRNA and tracrRNA were transcribed using T7 RNA polymerase from single-stranded DNA templates and hybridized as previously described (Jinek et al., 2012; Sternberg et al., 2014). L2 oligonucleotides (Table 3) were hybridized to generate the two different target DNA duplexes and native PAGE-purified before 5′ radiolabeling using [γ-³²P]-ATP (Perkin-Elmer) and T4 polynucleotide kinase (New England Biosciences).

Cleavage assays were carried out essentially as previously described (Sternberg et al., 2014). In brief, Cas9 and crRNA:tracrRNA were allowed to form an RNP complex before addition of target DNA. Final concentration of RNP was 100 nM and target was 1 nM. Reactions were incubated at room temperature, and aliquots were taken at 0.25, 0.5, 1, 2, 5, 10, 30, and 60 minutes and quenched by addition of an equal volume of 95% formamide and 50 mM EDTA. Samples were run on 10% urea-PAGE, visualized by phosphorimaging, and quantified using ImageQuant (GE Healthcare).

Plasmid Construction

All cloning was performed using chemically competent S. aureus cells, as previously described (Goldberg et al., 2014). The sequences of all the oligonucleotides used in for plasmid construction are in Table 3. Bsal cloning was used to construct pRH065 and pRH079 by inserting TAG (annealed primers H024-H025 containing compatible Bsal overhangs) and NGG-adjacent (H029-H030) spacers targeting ϕNM4γ4 into pDB114 (Bikard et al., 2014). The mutant cas9 library was constructed via 2-piece Gibson assembly (Gibson et al., 2009) by replacing wild-type cas9 on pRH065 with error-prone cas9 amplicons using primer pairs H294-H295 and H293-H296, respectively. The I473F mutation (codon ATT to TTT) was introduced on pRH065, pRH079, pWJ40 (Goldberg et al., 2014) and pDB114 by around-the-horn PCR (Moore and Prevelige, 2002) with primer pair H103-H104 to create plasmids pRH096, pRH176, pRH180 and pRH305. Bsal cloning was used to construct pRH306, pRH307 and pRH308 by inserting AAG (H546-H547), GAG (H548-H549) and CAG (H550-H551)-adjacent spacers targeting ϕNM4γ4 into pRH305. In addition, mutations R425G (AGA to GGA), I473A (ATT to GCT), K5001 (AAA to ATA), S701G (AGT to GGT), P756L (CCA to CTA) and A1032G (GCA to GGA) were each introduced on both pRH065 and pWJ40 by around-the-horn PCR with primer pairs H101-H102, H207-H208, H105-H106, H107-H108, H109-H110 and H111-H112 respectively. The randomized pWJ40 and pRH180 leader-barcoded libraries used for MiSeq were each constructed by 2-piece Gibson assembly with primers pairs H378-H294 and H379-H293.

Plasmid Loss Assays

To assess plasmid loss, cultures carrying the full S. pyogenes CRISPR system (expressing wtCas9 or hCas9) were passaged in the absence of phage for 10 days. Each day, the cultures were diluted 1:100 in fresh media with no antibiotics. At the end of the experiment, dilutions of the cells were plated on plates without antibiotic (to count the total number of cells) and with antibiotic (to count the number of cells that still carried the pCRISPR plasmids).

Cas9 Competition Assays

Plasmids pWJ40 and pRH180 carrying the full S. pyogenes CRISPR system (expressing wtCas9 and hCas9, respectively) were transformed into S. aureus RN4220 (no antibiotic resistance) and OS2 (erythromycin resistance), respectively. Overnight cultures of RN4220:pWJ40 and OS2:pRH180 launched from single colonies were diluted 1:100 in BHI. After 1 hour of growth, optical density at 600 nm (0D600) was measured for each culture, and samples were brought to equal cell densities. The two cultures were mixed in a 1:1 ratio and passaged for 5 days. Every day, the mixed culture was diluted 1:100 in fresh media and dilutions of the cells were plated on plates with chloramphenicol (to count the total number of cells) and plates with chloramphenicol and erythromycin (to count the number of cells that carried the hCas9 plasmid).

Protein Sequence Alignments

Amino acid sequences of Cas9 were obtained from the NCBI Protein database and aligned with Clustal Omega (www.ebi.ac.uk/Tools/msa/clustalo/). Alignments were visualized with Jalview (Waterhouse et al., 2009).

REFERENCES FOR THIS EXAMPLE

-   Bikard, D., Euler, C. W., Jiang, W., Nussenzweig, P. M.,     Goldberg, G. W., Duportet, X., Fischetti, V. A., and     Marraffini, L. A. (2014). Exploiting CRISPR-Cas nucleases to produce     sequence-specific antimicrobials. Nat Biotechnol 32, 1146-1150. -   Gibson, D. G., Young, L., Chuang, R. Y., Venter, J. C.,     Hutchison, C. A., 3rd, and Smith, H. O. (2009). Enzymatic assembly     of DNA molecules up to several hundred kilobases. Nat Methods 6,     343-345. -   Goldberg, G. W., Jiang, W., Bikard, D., and Marraffini, L. A.     (2014). Conditional tolerance of temperate phages via     transcription-dependent CRISPR-Cas targeting. Nature 514, 633-637. -   Heler, R., Samai, P., Modell, J. W., Weiner, C., Goldberg, G. W.,     Bikard, D., and Marraffini, L. A. (2015). Cas9 specifies functional     viral targets during CRISPR-Cas adaptation. Nature 519, 199-202. -   Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and     Charpentier, E. (2012). A programmable dual-RNA-guided DNA     endonuclease in adaptive bacterial immunity. Science 337,816-821. -   Mazmanian, S. K., Liu, G., Jensen, E. R., Lenoy, E., and     Schneewind, 0. (2000). Staphylococcus aureus sortase mutants     defective in the display of surface proteins and in the pathogenesis     of animal infections. Proc Natl Acad Sci USA 97, 5510-5515. -   Moore, S. D., and Prevelige, P. E., Jr. (2002). A P22 scaffold     protein mutation increases the robustness of head assembly in the     presence of excess portal protein. J Virol 76, 10245-10255. -   Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., and     Doudna, J. A. (2014). DNA interrogation by the CRISPR RNA-guided     endonuclease Cas9. Nature 507, 62-67. -   Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M., and     Barton, G. J. (2009). Jalview Version 2—a multiple sequence     alignment editor and analysis workbench. Bioinformatics 25,     1189-1191.

TABLE 1 Related to FIG. 2. Spacer sequences acquired by wtCas9- expressing cells. Location SEQ on ID Strain Sequence PAM φNM4y4 Strand NO RH71 ataaataaaaaagttactactcacacacta agg  258 −  2 RH64 cgaactaggaagaaaaatcgccatcaattca agg  453 −  3 RH69 aatagagatactttatctaacatgatacac ggg  805 +  4 RH51 tgatacacgggagaacaaaaccatcctacc cgg  827 +  5 RH99 tgatacacgggagaacaaaaccatcctacc cgg  827 +  6 RH47 gagaacaaaaccatcctacccggtaataaa tgg  837 +  7 RH107 tttattttgcgttagaattgacacctcaaga agg  873 +  8 RH127 tttattttgcgttagaattgacacctcaaga agg  873 +  9 RH57-2 tttattttgcgttagaattgacacctcaaga agg  873 + 10 RH57-1 tttagcgatattaattatgctcgtaagaat cgg 1241 + 11 RH63 agtattggaatctgatgaatattcatctct cgg 1423 − 12 RH40 aaaaatgttttaacacctattaacgtagtat tgg 1448 − 13 RH85 aatattcatcagattccaatactacgttaat agg 1461 + 14 RH36 ttcttcgcctctatatgtgttttctggtgt tgg 2810 − 15 RH109 acaaatttttcttcgcctctatatgtgttttc tgg 2816 − 16 RH10 ccaatttagaaatattaatcagagtgcctgt tgg 2981 − 17 RH42 agaaaatttatacattgattattcaccaac agg 2983 + 18 RH7 gctaagactgtgaagcataatactgctact agg 3087 − 19 RH33 gctaagactgtgaagcataatactgctact agg 3087 − 20 RH8 ttttaagctattcattttaaaaggtcatat ggg 3400 + 21 RH42 gtgttctcttcaatccattcatctattgct tgg 3502 − 22 RH85 atgaatggattgaagagaacacagacgaac agg 3540 + 23 RH120 ggagtaactaatatctgaattgttatcagt tgg 3650 − 24 RH97 attagttactccacaaatagaaatagagct agg 3698 + 25 RH86 ccacaaatagaaatagagctagggagtttaa cgg 3709 + 26 RH83 tagttttttgagtatgcttactttttcttg tgg 3822 − 27 RH32 acgaaagcgtctttatctcttgtagcaaacg tgg 3934 − 28 RH30 aaataagtctaaaaaaccaacgtttaatgat tgg 4197 + 29 RH52 aaataagtctaaaaaaccaacgtttaatgat tgg 4197 + 30 RH55-2 gaacgaattgtcagtatgtacagattaat agg 4241 + 31 RH55-1 aagaagaatacaaattccactttgttattac agg 4283 + 32 RH11 gcattacggacgtagtagaagcaattagaaa tgg 4577 + 33 RH26-1 aaaaacaattgattgaattagttactcgatt agg 4866 + 34 RH44 tagcttagattttgataccaatgatcttat tgg 4917 + 35 RH77 tagcttagattttgataccaatgatcttat tgg 4917 + 36 RH25 cggatttttcatttattaaaccttacaaaa agg 5009 + 37 RH115 tggatatgacgaccaagatttagcgtttta agg 5166 + 38 RH71 ataacgacggtacttattccgtcgttgctac tgg 5238 + 39 RH36 taatacaggtttttacaaaagctttaccat agg 5991 + 40 RH16-1 ctttaaatgttttaaaagaatagcatcatt tgg 6436 + 41

TABLE 2 Related to FIG. 2. Spacer sequences acquired by hCas9- expressing cells. Location SEQ on ID Strain Sequence PAM φNM4y4 Strand NO RH213 aatagagatactttatctaacatgatacac ggg  805 + 42 RH214 tgatacacgggagaacaaaaccatcctacc cgg  827 + 43 RH177 gagaacaaaaccatcctacccggtaataaa tgg  837 + 44 RH193 agtattggaatctgatgaatattcatctct cgg 1423 − 45 RH216 aaaaatgttttaacacctattaacgtagtat tgg 1448 − 46 RH206 aatattcatcagattccaatactacgttaat agg 1461 + 47 RH166 ttcttcgcctctatatgtgttttctggtgt tgg 2810 − 48 RH199 aaataagtctaaaaaaccaacgtttaatgat tgg 4197 + 49 RH174 aataagatcattggtatcaaaatctaagct agg 4889 − 50 RH195 cggatttttcatttattaaaccttacaaaa agg 5009 + 51 RH210 cggatttttcatttattaaaccttacaaaa agg 5009 + 52 RH187 cgacataacgctaatacatgtttgtcatag tgg 5695 − 53 RH205 taatacaggtttttacaaaagctttaccat agg 5991 + 54 RH211 tttttatttaagtattcgataatttctttata ggg 7355 − 55 RH202 tgtatgtcgctttgatacgatccatcaacat tgg 8123 − 56 RH175 attagacttttactttccattacttaaatca tgg 9043 + 57 RH215 attagacttttactttccattacttaaatca tgg 9043 + 58 RH164 ctaatactgttttaattaagttatcgatatc cgg 9097 − 59 RH185 atttatatccgatcttatacgaagtaaaga agg 13617 + 60 RH208 gcaaagttgagcgatcagtctgatttgatg agg 13783 + 61 RH200 ggaatatgatagcaattcaattgcacagta tgg 13911 + 62 RH203 aaaatgcaagaattaaactacccaccatat agg 14402 − 63 RH169 gataaaatcaaacaacttcacgacgcaataa cgg 15028 + 64 RH198 gataaaatcaaacaacttcacgacgcaataa cgg 15028 + 65 RH197 cgagtccaacacgtcatcaaattcttttat agg 16180 − 66 RH168 atatacacacatactaaacctgaacgatta agg 16252 + 67 RH209 tatgtgactctattagagcctcaatatgctt agg 16314 − 68 RH178 taagaatatagatccctataatgttatttttgt tgg 16769 + 69 RH189 gaatatagatccctataatgttatttttgt tgg 16769 + 70 RH176 ctcatcaatatcattctgattggttatttt ggg 17669 − 71 RH179 attgaaaaagatacgtatgcacattacaca agg 18135 + 72 RH204 ctaagatagctaaagcaatacgtgatgatgt cgg 18192 + 73 RH196 gaacacgtgatactcatcgtcatttagatg ggg 18365 + 74 RH180 ctaatcctttcgaatgataacgatctaattc agg 19067 − 75 RH173 tttgatgaaattttagttgttcagatgtagt agg 21085 − 76 RH192 taaactactacgacttaagcaggtgccata tgg 21278 + 77 RH212 taaactactacgacttaagcaggtgccata tgg 21278 + 78 RH201 aaaaataaggcaactgacagctagatattt agg 23282 + 79 RH165 tccattttgctgttgattcttctatgctatc cgg 37541 − 80 RH170 cctacgaatatgaacgacacaaatgattta ggg 38151 + 81

TABLE 3 Oligonucleotides used in this study. SEQ ID Name Sequence NO H024 aaacaaaaacaaaaatgttttaacacctattaacgg  82 H025 aaaaccgttaataggtgttaaaacatttttgttttt  83 H029 aaacaaaaatgttttaacacctattaacgtagtatg  84 H030 aaaacatactacgttaataggtgttaaaacattttt  85 H050 aaaacaaaaagcgcaagaagaaatcaaccagcgca  86 H052 aaaacttttttacaaattgagttatgttcatataa  87 H101 gctattttgagaggacaagaagacttttatcc  88 H102 ggataaaagtcttcttgtcctctcaaaatagc  89 H103 ggaagtctgaagaaacatttaccccatgg  90 H104 ccatggggtaaatgtttcttcagacttcc  91 H105 gacaaactttgatataaatcttccaaatgaaaaagtactacc  92 H106 ggtagtactttttcatttggaagatttatatcaaagtttgtc  93 H107 ccatgatgatggtttgacatttaaagaagac  94 H108 gtcttctttaaatgtcaaaccatcatcatgg  95 H109 gggcggcataagctagaaaatatcg  96 H110 cgatattttctagcttatgccgccc  97 H111 gcaagaaataggcaaaggaaccgc  98 H112 gcggttcctttgcctatttcttgc  99 H207 ggaagtctgaagaaacagctaccccatgg 100 H208 ccatggggtagctgtttcttcagacttcc 101 H293 gcaaaaatggataagaaatactcaataggc 102 H294 tattgagtatttcttatccatttttgcctcc 103 H295 aacacgcattgatttgagtcagc 104 H296 tcctagctgactcaaatcaatgcg 105 H372 nnnnnactaggggcttttcaagactg 106 H373 nnnnnactgaagaaatcaaccagcgc 107 H374 nnnnnctgaggggcttttcaagactg 108 H375 nnnnnctggaagaaatcaaccagcgc 109 H376 nnnnntgaaggggcttttcaagactg 110 H377 nnnnntgagaagaaatcaaccagcgc 111 H378 caggggcttttcaagactgnnnnnnnnnngagacaaatagtgcg 112 H379 cagtcttgaaaagcccctg 113 H546 aaactgaatattcatctctcggtatatataatccg 114 H547 aaaacggattatatataccgagagatgaatattca 115 H548 aaacccagaagttatgatagctaattcgtcatcag 116 H549 aaaactgatgacgaattagctatcataacttctgg 117 H550 aaacatgctccaatcgataaacaattagataaacg 118 H551 aaaacgtttatctaattgtttatcgattggagcat 119 L400 cgaaattttttagacaaaaatagtc 120 L2 Target gagtggaaggatgccagtgataagtggaatgccatgtgggctgtcaaaattgagc 121 L2 RC gctcaattttgacagcccacatggcattccacttatcactggcatccttccactc 122 L2 AG gagtggaaggatgccagtgataagtggaatgccatgtaggctgtcaaaattgagc 123 PAM L2 AG RC gctcaattttgacagcctacatggcattccacttatcactggcatccttccactc 124 L2 crRNA gugauaaguggaaugccaugguuuuagagcuaugcuguuuug 125 tracrRNA ggacagcauagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggca 126 ccgagucggugcuuuuu    L1 sgRNA gacgcauaaagaugagacgcguuuuagagcuaugcuguuuuggaaacaaaacagca 127 uagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucg gugcuuuuuuuggauc

While the invention has been described through specific embodiments, routine modifications will be apparent to those skilled in the art and such modifications are intended to be within the scope of the present invention. 

1. An expression vector encoding a Cas9 enzyme comprising a substitution, wherein the substitution is of at least one of the following amino acids: 1473 and K500.
 2. The expression vector of claim 1, wherein relative to a control the Cas9 enzyme exhibits at least one of: i) increased rate of spacer acquisition, or ii) increased cleavage efficiency of targets with NAG PAMs.
 3. The expression vector of claim 1, wherein the Cas9 is a Streptococcus pyogenes Cas9.
 4. The expression vector of claim 2, wherein the amino acid sequence of the Cas9 is at least 80% similar to SEQ ID NO:1 across its entire length.
 5. The expression vector of claim 4, wherein the substitution comprises I473F or K500I or a combination thereof.
 6. The expression vector of claim 4, wherein the substitution comprises the I473F.
 7. The expression vector of claim 4, wherein the substitution comprises the I473F and the K5001.
 8. Bacteria comprising an expression vector of claim
 1. 9. A method of making modified bacteria comprising introducing into the bacteria an expression of claim
 7. 10. A method comprising contacting bacteria of claim 8 with one or more bacteriophage such that at least one spacer sequence in the genome of the bacteriophage is acquired by the bacteria.
 11. The method of claim 10, wherein the bacteria are contacted with a plurality of distinct bacteriophage, and wherein the bacteria acquire a plurality of distinct spacer sequences from the plurality of the bacteriophage, and wherein the number of distinct spacers in the plurality is greater that a control value, and/or the distinct spacers in the plurality are acquired more quickly than for a control value.
 12. The method of claim 10, wherein the bacteriophage are obtained from a bacterial culture used to produce a food product or a beverage.
 13. The method of claim 12, wherein the food product comprises a dairy product.
 14. A food product comprising bacteria of claim
 8. 15. The food product of claim 14, wherein the food product comprises the dairy product.
 16. A method for labeling bacteria with one or more spacer sequences, the method comprising introducing into the bacteria an expression vector of claim 1, and introducing into the bacteria a polynucleotide comprising at least one spacer sequence.
 17. The method of claim 16, further comprising determining the sequence of at least one spacer sequence from bacteria that acquired the spacer sequence.
 18. A Cas9 enzyme comprising an amino acid substitution, wherein the amino acid substitution is of at least one of the following amino acids: 1473 and K500.
 19. The Cas9 enzyme of claim 18, wherein the Cas9 enzyme is a Streptococcus pyogenes Cas9 enzyme.
 20. The Cas9 enzyme of claim 18, wherein the Cas9 enzyme wherein the amino acid sequence of the Cas9 is at least 80% similar to SEQ ID NO:1 across its entire length. 